microsoft
/
InnerEye-DICOM-RT
зеркало из
1
0
Форкнуть 0
Код Задачи Пакеты Проекты Релизы Вики Активность

Fix DICOM Eclipse Issue (#16) 

* Update DICOM file saving

* 🚨 Fix flake8 linting
This commit is contained in:
Peter Hessey 2022-10-12 16:19:50 +01:00 коммит произвёл GitHub
Родитель e7f56ecec8
Коммит 9d3b618652
Не найден ключ, соответствующий данной подписи
Идентификатор ключа GPG: 4AEE18F83AFDEB23
5 изменённых файлов: 187 добавлений и 202 удалений
Показать статистику Скачать Patch файл Скачать Diff файл Показать все файлы Свернуть все файлы

4
RTConvert/Microsoft.RTConvert.Converters.Tests/RTEncodingTests.cs
Просмотреть файл

@ -52,15 +52,13 @@ namespace Microsoft.RTConvert.Converters.Tests
var outputEncoder = new DicomRTStructOutputEncoder();
var outputStructureBytes = outputEncoder.EncodeStructures(
var dcm = outputEncoder.EncodeStructures(
volumesWithMetadata,
new Dictionary<string, MedicalVolume>() { { "", referenceVolume } },
"modelX:1",
"manufacturer",
"interpreter");
var dcm = DicomFile.Open(new MemoryStream(outputStructureBytes.Array));
// Check the output format (should be RT struct)
Assert.AreEqual(DicomUID.RTStructureSetStorage, dcm.FileMetaInfo.MediaStorageSOPClassUID);

18
RTConvert/Microsoft.RTConvert.Converters/DicomRTStructOutputEncoder.cs
Просмотреть файл

@ -23,7 +23,7 @@ namespace Microsoft.RTConvert.Converters
public SegmentationOutputEncoding OutputEncoding => SegmentationOutputEncoding.RTStruct;
public ArraySegment<byte> EncodeStructures(
public DicomFile EncodeStructures(
IEnumerable<(string name, Volume3D<byte> volume, RGBColor color, bool fillHoles, ROIInterpretedType roiInterpretedType)> outputStructuresWithMetadata,
IReadOnlyDictionary<string, MedicalVolume> inputChannels,
string modelNameAndVersion,
@ -40,21 +40,7 @@ namespace Microsoft.RTConvert.Converters
manufacturer,
interpreter);
return SerializeDicomFile(structureSetFile);
}
private static ArraySegment<byte> SerializeDicomFile(DicomFile structureSetFile)
{
using (var memoryStream = new MemoryStream())
{
structureSetFile.Save(memoryStream);
if (!memoryStream.TryGetBuffer(out ArraySegment<byte> output))
{
throw new InvalidOperationException("Could not extract Array-Segment instance from Memory-Stream");
}
return output;
}
return structureSetFile;
}
private static DicomFile CreateStructureSetFile(

5
RTConvert/Microsoft.RTConvert.Converters/ISegmentationOutputEncoder.cs
Просмотреть файл

@ -3,6 +3,7 @@
namespace Microsoft.RTConvert.Converters
{
using Dicom;
using Microsoft.RTConvert.MedIO.Models;
using Microsoft.RTConvert.MedIO.RT;
using Microsoft.RTConvert.Models;
@ -40,7 +41,7 @@ namespace Microsoft.RTConvert.Converters
SegmentationOutputEncoding OutputEncoding { get; }
/// <summary>
/// Encodes the segmentation output in a binary format.
/// Encodes the segmentation output into a DicomFile object.
/// </summary>
/// <param name="outputStructures">The output structures from eh machine learning</param>
/// <param name="inputChannels">The input channels that were used to generate the structures</param>
@ -48,7 +49,7 @@ namespace Microsoft.RTConvert.Converters
/// <param name="manufacturer">The creator of the model.</param>
/// <param name="interpreter">The interpreter of the model.</param>
/// <returns></returns>
ArraySegment<byte> EncodeStructures(
DicomFile EncodeStructures(
IEnumerable<(string name, Volume3D<byte> volume, RGBColor color, bool fillHoles, ROIInterpretedType roiInterpretedType)> outputStructures,
IReadOnlyDictionary<string, MedicalVolume> inputChannels,
string modelAndVersion,

4
RTConvert/Microsoft.RTConvert.Converters/RTConverters.cs
Просмотреть файл

@ -275,14 +275,14 @@ namespace Microsoft.RTConvert.Converters
var outputEncoder = new DicomRTStructOutputEncoder();
var outputStructureBytes = outputEncoder.EncodeStructures(
var outputDicomFile = outputEncoder.EncodeStructures(
volumesWithMetadata,
new Dictionary<string, MedicalVolume>() { { "", referenceVolume } },
modelNameAndVersion,
manufacturer,
interpreter);
File.WriteAllBytes(dcmFilename, outputStructureBytes.Array);
outputDicomFile.Save(dcmFilename);
}
}
}

358
tests/test_nifti_to_dicom_rt_converter.py
Просмотреть файл

@ -1,179 +1,179 @@
# ------------------------------------------------------------------------------------------
# Copyright (c) Microsoft Corporation. All rights reserved.
# Licensed under the MIT License (MIT). See LICENSE in the repo root for license information.
# ------------------------------------------------------------------------------------------
"""
Tests for nifti_to_dicom_rt_converter.
"""
import logging
from pathlib import Path
from typing import List
from pydicom import dcmread
try:
from InnerEye_DICOM_RT.nifti_to_dicom_rt_converter import echo, get_version, rtconvert # type: ignore
except ImportError:
logging.info("using local src")
from src.InnerEye_DICOM_RT.nifti_to_dicom_rt_converter import echo, get_version, rtconvert # type: ignore
logger = logging.getLogger('test_rtconvert')
logger.setLevel(logging.DEBUG)
def test_get_version() -> None:
"""
Test that .dotnet core can be called --info and that it is
running version 2.1.
"""
(stdout, stderr) = get_version()
logger.debug("stdout: %s", stdout)
logger.debug("stderr: %s", stderr)
assert stderr == ''
assert 'Microsoft.NETCore.App 2.1.' in stdout
def test_echo() -> None:
"""
Test that the test Echo dll can be called and returns the test string and no error.
"""
test_string = "hello world2!"
(stdout, stderr) = echo(test_string)
logger.debug("stdout: %s", stdout)
logger.debug("stderr: %s", stderr)
assert stderr == ''
assert stdout == test_string + '\n'
def test_echo_err() -> None:
"""
Test that the test Echo dll can be called and returns the test and error strings.
"""
test_string = "hello world2!"
test_error = "Test error."
(stdout, stderr) = echo(test_string, test_error)
logger.debug("stdout: %s", stdout)
logger.debug("stderr: %s", stderr)
assert stderr == test_error + '\n'
assert stdout == test_string + '\n'
# The directory containing this file.
THIS_DIR: Path = Path(__file__).parent.resolve()
# The TestData directory.
TEST_DATA_DIR: Path = THIS_DIR / "TestData"
# Test Nifti file.
TestNiftiSegmentationLocation: Path = TEST_DATA_DIR / "hnsegmentation.nii.gz"
# Test reference series.
TestDicomVolumeLocation: Path = TEST_DATA_DIR / "HN"
# Target test output file.
TestOutputFile: Path = THIS_DIR / "test.dcm"
# Test fill holes.
FillHoles: List[bool] = [
True, True, True, True,
False, False, True, True,
True, True, False, True,
True, True, True, False,
True, False, True, True,
False, True
]
# Test ROIInterpretedType.
ROIInterpretedTypes: List[str] = [
"ORGAN", "None", "CTV", "EXTERNAL",
"ORGAN", "None", "CTV", "EXTERNAL",
"ORGAN", "None", "CTV", "EXTERNAL",
"ORGAN", "None", "CTV", "EXTERNAL",
"ORGAN", "None", "CTV", "EXTERNAL",
"ORGAN", "None"
]
# Test structure colors.
StructureColors: List[str] = [
"FF0001", "FF0002", "FF0003", "FF0004",
"FF0101", "FF0102", "FF0103", "FF0103",
"FF0201", "FF02FF", "FF0203", "FF0204",
"FF0301", "FF0302", "01FF03", "FF0304",
"FF0401", "00FFFF", "FF0403", "FF0404",
"FF0501", "FF0502"
]
# Test structure names.
StructureNames: List[str] = [
"External", "parotid_l", "parotid_r", "smg_l",
"smg_r", "spinal_cord", "brainstem", "globe_l",
"Globe_r", "mandible", "spc_muscle", "mpc_muscle",
"Cochlea_l", "cochlea_r", "lens_l", "lens_r",
"optic_chiasm", "optic_nerve_l", "optic_nerve_r", "pituitary_gland",
"lacrimal_gland_l", "lacrimal_gland_r"
]
Manufacturer = "Contosos"
Interpreter = "Ai"
ModelId = "XYZ:12"
def test_rtconvert() -> None:
"""
Test calling RTConvert for the test data.
"""
(stdout, stderr) = rtconvert(
in_file=TestNiftiSegmentationLocation,
reference_series=TestDicomVolumeLocation,
out_file=TestOutputFile,
struct_names=StructureNames,
struct_colors=StructureColors,
fill_holes=FillHoles,
roi_interpreted_types=ROIInterpretedTypes,
manufacturer=Manufacturer,
interpreter=Interpreter,
modelId=ModelId
)
logger.debug("stdout: %s", stdout)
logger.debug("stderr: %s", stderr)
assert stderr == ''
assert "Successfully written" in stdout
assert TestOutputFile.is_file()
with open(TestOutputFile, 'rb') as infile:
ds = dcmread(infile)
assert ds is not None
# Check the modality
assert ds.Modality == 'RTSTRUCT'
assert ds.Manufacturer == Manufacturer
assert ds.SoftwareVersions == ModelId
assert len(ds.StructureSetROISequence) == len(StructureNames)
for i, item in enumerate(StructureNames):
assert ds.StructureSetROISequence[i].ROINumber == i + 1
assert ds.StructureSetROISequence[i].ROIName == item
assert Interpreter in ds.RTROIObservationsSequence[i].ROIInterpreter
assert ds.RTROIObservationsSequence[i].RTROIInterpretedType == ('' if ROIInterpretedTypes[i] == 'None' else ROIInterpretedTypes[i])
assert len(ds.ROIContourSequence) == len(StructureNames)
for i, item in enumerate(StructureNames):
assert ds.ROIContourSequence[i].ReferencedROINumber == i + 1
assert ds.ROIContourSequence[i].ROIDisplayColor == _parse_rgb(StructureColors[i])
def _parse_rgb(rgb: str) -> List[int]:
"""
Convert the string representation of RGB color to an int list
:param rgb: Color string
:return: List of [R, G, B] components.
"""
return [int(rgb[i:i+2], 16) for i in (0, 2, 4)]
# ------------------------------------------------------------------------------------------
# Copyright (c) Microsoft Corporation. All rights reserved.
# Licensed under the MIT License (MIT). See LICENSE in the repo root for license information.
# ------------------------------------------------------------------------------------------
"""
Tests for nifti_to_dicom_rt_converter.
"""
import logging
from pathlib import Path
from typing import List
from pydicom import dcmread
try:
from InnerEye_DICOM_RT.nifti_to_dicom_rt_converter import echo, get_version, rtconvert # type: ignore
except ImportError:
logging.info("using local src")
from src.InnerEye_DICOM_RT.nifti_to_dicom_rt_converter import echo, get_version, rtconvert # type: ignore
logger = logging.getLogger('test_rtconvert')
logger.setLevel(logging.DEBUG)
def test_get_version() -> None:
"""
Test that .dotnet core can be called --info and that it is
running version 2.1.
"""
(stdout, stderr) = get_version()
logger.debug("stdout: %s", stdout)
logger.debug("stderr: %s", stderr)
assert stderr == ''
assert 'Microsoft.NETCore.App 2.1.' in stdout
def test_echo() -> None:
"""
Test that the test Echo dll can be called and returns the test string and no error.
"""
test_string = "hello world2!"
(stdout, stderr) = echo(test_string)
logger.debug("stdout: %s", stdout)
logger.debug("stderr: %s", stderr)
assert stderr == ''
assert stdout == test_string + '\n'
def test_echo_err() -> None:
"""
Test that the test Echo dll can be called and returns the test and error strings.
"""
test_string = "hello world2!"
test_error = "Test error."
(stdout, stderr) = echo(test_string, test_error)
logger.debug("stdout: %s", stdout)
logger.debug("stderr: %s", stderr)
assert stderr == test_error + '\n'
assert stdout == test_string + '\n'
# The directory containing this file.
THIS_DIR: Path = Path(__file__).parent.resolve()
# The TestData directory.
TEST_DATA_DIR: Path = THIS_DIR / "TestData"
# Test Nifti file.
TestNiftiSegmentationLocation: Path = TEST_DATA_DIR / "hnsegmentation.nii.gz"
# Test reference series.
TestDicomVolumeLocation: Path = TEST_DATA_DIR / "HN"
# Target test output file.
TestOutputFile: Path = THIS_DIR / "test.dcm"
# Test fill holes.
FillHoles: List[bool] = [
True, True, True, True,
False, False, True, True,
True, True, False, True,
True, True, True, False,
True, False, True, True,
False, True
]
# Test ROIInterpretedType.
ROIInterpretedTypes: List[str] = [
"ORGAN", "None", "CTV", "EXTERNAL",
"ORGAN", "None", "CTV", "EXTERNAL",
"ORGAN", "None", "CTV", "EXTERNAL",
"ORGAN", "None", "CTV", "EXTERNAL",
"ORGAN", "None", "CTV", "EXTERNAL",
"ORGAN", "None"
]
# Test structure colors.
StructureColors: List[str] = [
"FF0001", "FF0002", "FF0003", "FF0004",
"FF0101", "FF0102", "FF0103", "FF0103",
"FF0201", "FF02FF", "FF0203", "FF0204",
"FF0301", "FF0302", "01FF03", "FF0304",
"FF0401", "00FFFF", "FF0403", "FF0404",
"FF0501", "FF0502"
]
# Test structure names.
StructureNames: List[str] = [
"External", "parotid_l", "parotid_r", "smg_l",
"smg_r", "spinal_cord", "brainstem", "globe_l",
"Globe_r", "mandible", "spc_muscle", "mpc_muscle",
"Cochlea_l", "cochlea_r", "lens_l", "lens_r",
"optic_chiasm", "optic_nerve_l", "optic_nerve_r", "pituitary_gland",
"lacrimal_gland_l", "lacrimal_gland_r"
]
Manufacturer = "Contosos"
Interpreter = "Ai"
ModelId = "XYZ:12"
def test_rtconvert() -> None:
"""
Test calling RTConvert for the test data.
"""
(stdout, stderr) = rtconvert(
in_file=TestNiftiSegmentationLocation,
reference_series=TestDicomVolumeLocation,
out_file=TestOutputFile,
struct_names=StructureNames,
struct_colors=StructureColors,
fill_holes=FillHoles,
roi_interpreted_types=ROIInterpretedTypes,
manufacturer=Manufacturer,
interpreter=Interpreter,
modelId=ModelId
)
logger.debug("stdout: %s", stdout)
logger.debug("stderr: %s", stderr)
assert stderr == ''
assert "Successfully written" in stdout
assert TestOutputFile.is_file()
with open(TestOutputFile, 'rb') as infile:
ds = dcmread(infile)
assert ds is not None
# Check the modality
assert ds.Modality == 'RTSTRUCT'
assert ds.Manufacturer == Manufacturer
assert ds.SoftwareVersions == ModelId
assert len(ds.StructureSetROISequence) == len(StructureNames)
for i, item in enumerate(StructureNames):
assert ds.StructureSetROISequence[i].ROINumber == i + 1
assert ds.StructureSetROISequence[i].ROIName == item
assert Interpreter in ds.RTROIObservationsSequence[i].ROIInterpreter
assert ds.RTROIObservationsSequence[i].RTROIInterpretedType == ('' if ROIInterpretedTypes[i] == 'None' else ROIInterpretedTypes[i])
assert len(ds.ROIContourSequence) == len(StructureNames)
for i, item in enumerate(StructureNames):
assert ds.ROIContourSequence[i].ReferencedROINumber == i + 1
assert ds.ROIContourSequence[i].ROIDisplayColor == _parse_rgb(StructureColors[i])
def _parse_rgb(rgb: str) -> List[int]:
"""
Convert the string representation of RGB color to an int list
:param rgb: Color string
:return: List of [R, G, B] components.
"""
return [int(rgb[i:i+2], 16) for i in (0, 2, 4)]